[gmx-users] Steered Molecular Dynamics (SMD)
Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I expected. Part of my .gro file and .mdp file are below. By using them, the COM of the slab of griphene moved at a constant speed, but the 'slab' crashed. Because not all the carbon atoms moved at the same speed. In order to produce the results that I want, which pull type (no, umbrella, constraint or constant_force) and which pull geometry (distance, direction, cylinder or position) shall I use? There is no reference group in my simulation. Do I need to modify the .gro file? Part of the .gro file: ... 4917sla C11093 1.265 1.609 0.237 4918sla C11094 1.549 1.609 0.237 4919sla C11095 1.336 1.486 0.237 4920sla C11096 1.478 1.486 0.237 4921sla C11097 1.691 1.363 0.237 4922sla C11098 1.975 1.363 0.237 4923sla C11099 1.762 1.240 0.237 4924sla C11100 1.904 1.240 0.237 4925sla C11101 2.117 1.363 0.237 4926sla C11102 2.401 1.363 0.237 ... These are all the carbon atoms of the slab of griphene. The Pulling Code: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= direction ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 10 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = pull_weights0= pull_pbcatom0= 0 pull_group1 = sla pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.237 pull_rate1 = 5e-4 pull_k1 = pull_kB1 = Any suggestions are welcome! Thank you in advance!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5
Hi, you should set one pull group, not 700. The number of atoms in your pull group is 700. Freezing the pull group in x and y direction probably does what you want. Please also consider to upgrade to 4.0.7, which is the most recent stable version. Best, Carsten On Jan 22, 2010, at 7:41 AM, toby10222...@sina.com wrote: Dear all: I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y direction. The following is the PULL CODE in my mdp file. However, when I used this code for my simulation the error always came out as “Number of weights (1) for pull group 1 'sla' does not match the number of atoms (700)”. So here are my doubts about this simulation: 1. Can Gromacs-4.0.5 do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction? 2. In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right? 3. How to give the “pull_weights1” to avoid the above ERROR? Any suggestions and answers are welcome. Thank you in advance! ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constant_force ; Pull geometry: distance, direction, cylinder or position pull_geometry= distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 10 ; Number of pull groups pull_ngroups = 700 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = pull_weights0= pull_pbcatom0= pull_group1 = sla pull_weights1= 1 pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.0 pull_rate1 = 0 pull_k1 = 1.2e-4 pull_kB1 = 0 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5
nbsp; Dear all: nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y direction. The following is the PULL CODE in my mdp file. However, when I used this code for my simulation the error always came out as “Number of weights (1) for pull group 1 'sla' does not match the number of atoms (700)”. So here are my doubts about this simulation: 1.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; Can Gromacs-4.0.5 do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction? 2.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right? 3.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; How to give the “pull_weights1” to avoid the above ERROR? Any suggestions and answers are welcome. Thank you in advance! nbsp; ; COM PULLINGnbsp; nbsp;nbsp; nbsp;nbsp; nbsp; ; Pull type: no, umbrella, constraint or constant_force pullnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= constant_force ; Pull geometry: distance, direction, cylinder or position pull_geometrynbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= distance ; Select components for the pull vector. default: Y Y Y pull_dimnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp;nbsp;= N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= ; Switch from r1 to r0 in case of dynamic reaction force pull_r0nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= pull_constr_tolnbsp; nbsp;nbsp; nbsp;nbsp; nbsp; = 1e-06 pull_startnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= no pull_nstxoutnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp; = 10 pull_nstfoutnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp; = 10 ; Number of pull groups pull_ngroupsnbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp; = 700 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp;nbsp;= pull_weights0nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= pull_pbcatom0nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= pull_group1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp;nbsp;= sla pull_weights1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= 1 pull_pbcatom1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= 0 pull_vec1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp; = 0.0 0.0 1.0 pull_init1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= 0.0 pull_rate1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= 0 pull_k1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;= 1.2e-4 pull_kB1nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp; nbsp;nbsp;nbsp;= 0-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
